Automated design of genomic Southern blot probes

Mike DR Croning, David G Fricker, Noboru H Komiyama and Seth GN Grant

Design Case - ProbeDesign53 - back to list

Summary
Image
Unique putative probes (0)
Putative probes (54)
Redundant probes (1)

Summary

`./analyse_probe_search_results : Mon Sep 26 11:57:28 2005`

Connected to host: host, as user: user
Database       : southern_blot_designs

Fetched probe design: ProbeDesign53
  assembly      : NCBIM34
  bias          : 3prime
  chromosome    : X
  id            : 38
  strand        : 1
  -------------

Design window length: 6001bp

All jobs for probe design are successful - total: 108
Fetched conf : Exonerate mouse_NCBIM34 (id: 1)
  Genome file(s) at: /blastdb/Mouse/NCBIM34/softmasked_dusted
Fetched 2146 putative probes to analyse

Selection criteria to rank probes:
  Minimum score ratio             : 10
  (i.e. self-hit must score at least 10 times higher than the next best hit)
  Maximum percent repetitive bases: 5
  Favour probes to the 3prime end of design window
  ------------------------

Putative probes without hits                : 0
Putative probes with single_self_hit        : 2146/2146
Putative probes exceeding selection criteria: 55/2146

PASSED (GREEN) AND FAILED PUTATIVE PROBES IN THE DESIGN WINDOW
--------------------------------------------------------------

Image

Unique (yellow), passed (green) and failed putative probes in the design window

Unique putative probes

No probes

Putative probes

Putative probe ID	Length	Score ratio	Actual	%rep DNA	Distance	Overall
41296	700	18.6	3500	-	3325	18.6
41297	700	18.6	3500	-	3360	18.6
41457	650	17.3	3250	-	3328	17.3
41458	650	17.3	3250	-	3360	17.3
41459	650	17.3	3250	-	3392	17.3
41149	750	19.9	3750	1.5	3330	17.0
41631	600	16.0	3000	-	3300	16.0
41632	600	16.0	3000	-	3330	16.0
41633	600	16.0	3000	-	3360	16.0
41634	600	16.0	3000	-	3390	16.0
41635	600	16.0	3000	-	3420	16.0
41636	600	16.0	3000	-	3450	16.0
41460	650	17.3	3250	0.8	3424	15.7
41825	550	14.6	2750	-	3321	14.6
41826	550	14.6	2750	-	3348	14.6
41827	550	14.6	2750	-	3375	14.6
41828	550	14.6	2750	-	3402	14.6
41829	550	14.6	2750	-	3429	14.6
41830	550	14.6	2750	-	3456	14.6
41831	550	14.6	2750	-	3483	14.6
41832	550	14.6	2750	-	3510	14.6
42036	500	13.3	2500	-	3300	13.3
42037	500	13.3	2500	-	3325	13.3
42038	500	13.3	2500	-	3350	13.3
42039	500	13.3	2500	-	3375	13.3
42040	500	13.3	2500	-	3400	13.3
42041	500	13.3	2500	-	3425	13.3
42042	500	13.3	2500	-	3450	13.3
42043	500	13.3	2500	-	3475	13.3
42044	500	13.3	2500	-	3500	13.3
42045	500	13.3	2500	-	3525	13.3
42046	500	13.3	2500	-	3550	13.3
40926	850	12.5	4250	-	5082	12.5
41055	800	11.8	4000	-	5080	11.8
41056	800	11.8	4000	-	5120	11.8
41298	700	18.6	3500	3.7	3395	11.2
41196	750	11.0	3750	-	5069	11.0
41197	750	11.0	3750	-	5106	11.0
41198	750	11.0	3750	-	5143	11.0
41199	750	11.0	3750	-	5180	11.0
42047	500	13.3	2500	1.2	3575	10.9
40803	900	10.3	4500	-	5040	10.3
41346	700	10.3	3500	-	5075	10.3
41347	700	10.3	3500	-	5110	10.3
41348	700	10.3	3500	-	5145	10.3
41349	700	10.3	3500	-	5180	10.3
41350	700	10.3	3500	-	5215	10.3
41351	700	10.3	3500	1.0	5250	8.3
41833	550	14.6	2750	3.3	3537	8.1
41057	800	11.8	4000	2.1	5160	7.5
40927	850	12.5	4250	3.6	5124	5.2
41200	750	11.0	3750	3.2	5217	4.6
40804	900	13.2	4500	4.7	5085	3.9
40690	950	10.1	4750	3.8	5029	2.5

Overall score = score_ratio - 2 * repetitive DNA content

Redundant probes

Putative probe ID	Length	Score ratio	Actual	%rep DNA	Distance	Overall
41637	600	16.0	3000	1.8	3480	12.3

Overall score = score_ratio - 2 * repetitive DNA content